R/SSDM.R

In SSDM: Stacked Species Distribution Modelling

#' SSDM: Stacked species distribution modelling
#'
#' SSDM is a package to map species richness and endemism based on Stacked Species Distribution Models (SSDM). It provides tools to build
#' SDM, i.e. a single species fitted with a single algorithm, Ensemble SDM (ESDM), i.e. a single species fitted with multiple algorithms,
#' SSDM several species with one or more algorithms. The package includes numerous modelling algorithms, and specifiable ensemble aggregating and stacking methods.
#' This package also provides tools to evaluate and explore models such as variable importance, algorithm accuracy, and between-algorithm
#' correlation, and tools to map results such as habitat suitability maps, binary maps, between-algorithm variance maps.
#' For ease of use, the SSDM package provides a user-friendly graphical interface (\code{\link{gui}}).
#'
#' The SSDM package provides five categories of functions (that you can find in details
#' below): Data preparation, Modelling main functions, Model main methods, Model
#' classes, and Miscellaneous.
#'
#' @section Data preparation: \describe{\item{\code{\link{load_occ}}}{Load
#'   occurrence data} \item{\code{\link{load_var}}}{Load environmental variables}}
#'
#' @section Modelling main  functions: \describe{
#'   \item{\code{\link{modelling}}}{Build an SDM using a single algorithm}
#'   \item{\code{\link{ensemble_modelling}}}{Build an SDM that assembles
#'   multiple algorithms} \item{\code{\link{stack_modelling}}}{Build an SSDMs
#'   that assembles multiple algorithms and species}}
#'
#' @section Model main methods: \describe{
#'   \item{\code{\link{ensemble,Algorithm.SDM-method}}}{Build an ensemble SDM}
#'   \item{\code{\link{stacking,Ensemble.SDM-method}}}{Build an SSDM}
#'   \item{\code{\link{update,Stacked.SDM-method}}}{Update a previous SSDM with
#'   new occurrence data}}
#'
#'
#' @section Model classes: \describe{
#'   \item{\code{\linkS4class{Algorithm.SDM}}}{S4 class to represent SDMs}
#'   \item{\code{\linkS4class{Ensemble.SDM}}}{S4 class to represent ensemble
#'   SDMs} \item{\code{\linkS4class{Stacked.SDM}}}{S4 class to represent SSDMs}}
#'
#' @section Miscellaneous: \describe{ \item{\code{\link{gui}}}{User-friendly
#'   interface for SSDM package} \item{\code{\link{plot.model}}}{Plot SDMs}
#'   \item{\code{\link{save.model}}}{Save SDMs}
#'   \item{\code{\link{load.model}}}{Load SDMs}}
#'
#' @docType package
#' @name SSDM
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